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Foot-and-mouth disease virus (FMDV) causes a severe infection in ruminant animals. Here we present an in-depth transcriptional analysis of soft-palate tissue from cattle experimentally infected with FMDV. The differentially expressed genes from two Indian cattle (Bos indicus) breeds (Malnad Gidda and Hallikar) and Holstein Friesian (HF) crossbred calves, highlighted the activation of metabolic processes, mitochondrial functions and significant enrichment of innate antiviral immune response pathways in the indigenous calves. The results of RT-qPCR based validation of 12 genes was in alignment with the transcriptome data. The indigenous calves showing lesser virus load, elicited early neutralizing antibodies and IFN-γ immune responses. This study revealed that induction of potent innate antiviral response and cell mediated immunity in indigenous cattle, especially Malnad Gidda, significantly restricted FMDV replication during acute infection. These data highlighting the molecular processes associated with host-pathogen interactions, could aid in the conception of novel strategies to prevent and control FMDV infection in cattle.

Deciphering sperm transcriptome is the key to understanding the molecular mechanisms governing peri-fertilization, embryonic development, and pregnancy establishment. This study aimed to profile sperm transcriptome to identify signature transcripts regulating male fertility. Semen samples were collected from 47 bulls with varied fertility rates. The sperm total RNA was isolated (n = 8) and subjected to transcriptome sequencing. Based on the expression pattern obtained from RNA profiling, the bulls were grouped (p = 0.03) into high-fertile and sub-fertile, and signature transcripts controlling sperm functions and fertility were identified. The results were validated using the OMIM database, qPCR, and sperm function tests. The sperm contains 1100 to 1700 intact transcripts, of which BCL2L11 and CAPZA3 were abundant and associated (p

The rumen wharves conglomerate of symbiotic fibrolytic microflora with the potential to produce repertoire of carbohydrate-active enzymes to elicit the degradation of recalcitrant plant lignocellulosic complex into simpler forms that can be utilized by the host. A metatranscriptomics approach was adopted to explore the metabolically active microbiota and the transcripts involved in the deconstruction of lignocellulose in Indian crossbred cattle rumen. The experimental animals were fed with mixed diet for a period of twenty-one days and the total RNA was isolated from the rumen digesta using a modified total RNA extraction protocol. After mRNA enrichment, the cDNA libraries were subjected to sequencing under Illumina HiSeq platform and generated about 2.89 GB of raw sequences. The contig assembly was accomplished using two different tools and the redundant sequences were removed before further processing. A total of 133,930 orfs were predicted from the assembled contigs using MetaGeneMark tool and the taxonomic affiliation of orfs were achieved using MEGAN 6.0 Community Edition. A total of 17 bacterial, 5 eukaryotic and 1 archaeal phylum were identified from rumen metatranscriptomic dataset. Phylum Bacteroidetes were acknowledged as the most abundant and metabolically active rumen bacterial populations in cattle rumen with 36,414 orfs corresponding to it, followed by Firmicutes with 6,349 orfs. Further, MEGAN annotation of metatranscriptomic data at species level revealed that Prevotella brevis and Prevotella ruminicola as the most metabolically active bacterial populations representing 4,022 and 2,725 orfs each. The functional annotation of metatranscriptomic data using COG database revealed that a large number of transcripts (~16%) were corresponding to translation, ribosomal structure and biogenesis and carbohydrate transport and metabolism (15%). dbCAN annotation of rumen metatranscriptomic data identified and classified 5,267 transcripts belonging to 168 CAZyme families (GH-52%, GT-26%, CBM-14%, CE-6%, PL-2% and AA-0%). The microbial community analysis of the CAZyme encoding transcripts using M5NR database revealed that a significant proportion of CAZymes were contributed by genera Prevotella (37%) and Bacteroides (21%). The cattle rumen microbiome metatranscriptome analysis presented in this study facilitated the detection of large number of transcripts encoding diverse CAZymes that actively take part in the hydrolysis of plant lignocellulose complex that may be useful for improving livestock and biofuel generation.

In vitro and in vivo studies were conducted to examine the effect of silkworm pupae oil on methane (CH4) emission and methanogens diversity. Five graded levels (2, 4, 6, 8 and 10%) of silkworm pupa...

The ability to identify the sex of embryo and control of sex ratio has a great commercial importance to livestock industry. Prediction of embryonic sex could be useful in the management decisions of sex selection in breeding programs. Several methods have been attempted to determine the sex but the polymerase chain reaction (PCR)-based sexing method is generally favoured, as it is cost effective, simple and reliable. The aim of the present study was to identify sex of sheep embryos produced in vitro through amplification of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), sex-determining region Y (SRY) and amelogenin genes present in genomic DNA (gDNA) of embryos through PCR. To avoid false interpretation of the result by no amplification of SRY in female embryos, a duplex PCR was approached to amplify combinedly SRY and GAPDH genes. Sex-specific blood was used in PCR as positive control. In vitro sheep embryos were produced as per standardized protocol of laboratory. Sexing of sex-specific blood and in vitro produced embryos were approached though PCR to amplify the respective genes using gDNA present in the sample without its traditional isolation. The accuracy of sex prediction for embryos was 100% by this procedure.

This study aimed to assess the effect of the insulin-like grow factor 1 (IGF-1) treatment during in vitro maturation on the gene expression and developmental ability of ovine oocytes. Ovine cumulus...

Aim: The present study was undertaken to evaluate the effect of variable levels of silkworm pupae oil and roughage: concentrate ratio on in vitro methane production, fermentation characteristics, and rumen protozoa population. Materials and Methods: In vitro gas production study (24 h) was performed with graded levels of silkworm pupae oil, namely, 0.5, 1, 2, 4, and 5% of the basal diet and four variable dietary regimes consisting roughage and concentrate in different proportions (70:30, 60:40, 50:50, and 40:60). At the end of incubation, gas samples were analyzed for methane, while fermented rumen liquor was used for protozoa enumeration. A separate set of incubations was carried out for the determination of in vitro dry matter digestibility. Results: Results from the in vitro studies revealed no adverse impact of the silkworm pupae oil supplementation up to 2% level on total gas production. However, supplementation beyond 2% has shown a reduction in total gas production. Incubation with variable levels (0.5-5%) of silkworm pupae oil with different dietary regimes indicated negligible (3-5%) to a substantial reduction (25-30%) on methane production. A graded decrement in methane production was recorded with increasing levels of silkworm pupae oil. Similarly, the protozoal populations were decreased from 10 to 51.5% with graded levels of silkworm pupae oil in different dietary regimes as studies did not reveal any significant (p>0.05) variation between 2 and 4% of oil supplementation. Conclusion: The silkworm pupae oil supplementation at 2% level decreases methane production by 12-15% without any adverse impact on feed fermentation. Oil supplementation may have a more pronounced effect on methane reduction if added to high roughage diet at in vitro conditions. However, in vivo, studies in ruminants are warranted to confirm the methane reduction with silkworm pupae oil supplementation.

The study aimed to compare the effect of individual or combined supplementation of condensed tannins (Tamarindus indica) and saponins-containing (Sapindus mukorossi) phyto-sources on enteric methan...

A study was conducted in eighteen sheep divided into three groups of six animals each and fed on a diet comprising finger millet (Eleusine coracana) straw and concentrate in 50:50. Animals in the c...

The current study aimed to assess the effect of different seasons (summer, monsoon and winter) on the quality, preservability and fertilizing ability of spermatozoa in Bannur rams. The level of hea...

Interleukin-7 (IL-7) mediated signals are linked to development, proliferation, survival and differentiation of cells. Recent evidences indicate its role in oocyte maturation process as well. Nevertheless, the underlying mechanisms of IL-7 involvement in oocyte maturation are not well characterized. In addition, currently no information is available on the effect of exogenous IL-7 on oocyte maturation in ovine or any other species. In this study, the effect of IL-7 supplementation during in vitro maturation (IVM) on the maturation rate, production of reactive oxygen species (ROS) and gene expression of ovine cumulus-oocyte complexes (COC) was assessed. IL-7 (0.5, 1, 2, 5 and 10 ng/ml) was supplemented in IVM medium at the beginning (0 h) and maturation rate of COC was assessed at the completion of IVM (24 h). The maturation rate (%) was found significantly (P = 0.000) greater with the 1 ng/ml of IL-7 supplementation (69.5) than control (60.0). In contrast, the maturation rate was reduced significantly (P = 0.000) with the 2 (47.1), 5 (39.2) and 10 ng/ml (39.1) of IL-7 as compared to the control. The level of intracellular ROS in the matured COC was found considerably higher with the 5 ng/ml of IL-7 followed by 1 ng/ml of IL-7 and control. It was evident that in the presence of superoxide dismutase-inhibitor, 1 ng/ml of IL-7 did not stimulate oocyte maturation. In contrast, oocyte maturation was improved with 5 ng/ml of IL-7 supplementation in the presence of NADPH-oxidase-inhibitor. IL-7 supplementation influenced gene expression in COC in a dose and time dependant manner. The expression of genes related to ROS production and apoptosis were upregulated and the genes associated with antioxidant mechanisms were downregulated noticeably with the supplementation of 5 ng/ml of IL-7. In conclusion, IL-7 at low concentration was beneficial for oocyte maturation, which was likely mediated through the favourable level of intracellular ROS and antioxidant mechanisms. In contrast, the detrimental effects of greater IL-7 concentrations on oocyte maturation were possibly arbitrated through the ROS-mediated oxidative stress, compromised antioxidant mechanism and stimulated apoptotic signalling.

Objective Ensiling of tannin-rich fruit byproducts (FB) involves quantitative and qualitative changes in the tannins, which would consequently change the rumen fermentation characteristics. This study aimed to evaluate whether ensiled FBs are effective in mitigating methane emission from ruminants by conducting in vitro assessments. Methods Fruit byproducts (grape pomace, wild grape pomace, and persimmon skin) were collected and subjected to four-week ensiling by Lactobacillus buchneri inoculant. A defined feed component with or without FB samples (both fresh and ensiled material) were subjected to in vitro anaerobic culturing using rumen fluid sampled from beef cattle, and the fermentation parameters and microbial populations were monitored. Results Reduced methane production and a proportional change in total volatile fatty acids (especially enhanced propionate proportion) was noted in bottles containing the FBs compared with that in the control (without FB). In addition, we found lower gene copy number of archaeal 16S rRNA and considerably higher levels of one of the major fibrolytic bacteria (Fibrobacter succinogenes) in the bottles containing FBs than in the control, particularly, when it was included in a forage-based feed. However, in the following cultivation experiment, we observed that FBs failed to exhibit a significant difference in methane production with or without polyethylene glycol, implying that tannins in the FBs may not be responsible for the mitigation of methane generation. Conclusion The results of the in vitro cultivation experiments indicated that not only the composition but also ensiling of FBs affected rumen fermentation patterns and the degree of methane generation. This is primarily because of the compositional changes in the fibrous fraction during ensiling as well as the presence of readily fermented substrates, whereas tannins in these FBs seemed to have little effect on the ruminal fermentation kinetics.

Basidiomycetes are of special interest in biotechnological research for their versatile potential in degradation of lignocellulosic biomass. This study accordingly reports analysis of transcriptome of a white-rot BasidiomyceteL.squarrosulusgrown in simple potato dextrose broth supplemented with aromatic compound, reactive black dye to gain an insight into the degradation ability of the fungus. RNA was sequenced using Illumina NextSeq 500 to obtain 6,679,162 high quality paired end reads that were assembledde novousing CLC assembly cell to generate 25,244 contigs.Putative functions were assigned for the 10,494 transcripts based on sequence similarities through BLAST2GO 5.2 and Function annotator. Functional assignments revealed enhanced oxidoreductase activity through the expression of diverse biomass degrading enzymes and their corresponding co-regulators. CAZyme analysis through dbCAN and CUPP revealed the presence of 6 families of polysaccharide lyases, 51 families of glycoside hydrolases, 23 families of glycoside transferases, 7 families of carbohydrate esterases and 10 families of Auxiliary activities.Genes encoding the ligninolytic enzymes and auxiliary activities among the transcript sequences were identified through gene prediction by AUGUSTUS and FGENESH. Biochemical analysis of a couple of biomass degrading enzymes substantiated the functional predictions. In essence,L.squarrosulusgrown in a simple medium devoid of lignocellulosic substrate demonstrated presence of a repertoire of lignocellulose degrading enzymesimplying that source of lignocellulose is not required for expression of these biomass degrading enzymes. The study hereby underlines the significance ofL.squarrosulusin biomass degradation and its future functional exploitation in biomass conversion applications.

Background Archaea belong to the domain Euryarchaeota, represents only 3-5% of the rumen microbiota; however, they play a central role in maintaining the H2 pressure. Host species in conjunction with geographical regions may lead to the variable distribution of rumen methanogens. Indian cattle and buffaloes represent 13 and 53% of the global population, respectively. However, the influence of host species (bovine) and geographical regions on the methanogens distribution has not been investigated in Indian subcontinent. Therefore, the present study was undertaken to explore the rumen methanogens diversity in the cattle and buffaloes native to the two distinct geographical regions of India. Results Next generation sequencing of 16S rRNA gene from 36 rumen fluid samples corresponding to cattle and buffaloes revealed that Methanobrevibacter (Mbr.) genus constituted largest fraction (55-62%) of the rumen archaeal community. Furthermore, Methanobrevibacter gottschalkii was the most prominent methanogens with the significantly higher abundance in cattle. Methanomassiliicoccales represented Methanomassiliicoccales, such as Methanosphaera sp., Group 4, Group 8, Group 12 sp. and Group 9 sp. was significantly higher in cattle. The distribution of prominent methanogens, such as Mbr. gottschalkii and Mbr. ruminantium did not differ between two host species in the north region. However, Mbr. gottschalkii was significantly higher in buffaloes as compared to cattle in south region. Mbr. wolinii was exclusively detected in the cattle. Inter-region comparison established that Methanomassiliicoccales were the most variable between the two regions. Conclusions Host species did not affect the distribution of hydrogenotrophic methanogens except for Mbr. gottschalkii. Methylotrophic methanogens, in spite of their limited representation, were most influenced by the host species and geographical regions. Overall, the Methanomassiliicoccales distribution was higher in cattle, and the environmental conditions in north region were conducive for their higher distribution. The variable distribution of methanogens indicated that host and geographical region oriented strategies needs to be developed for the reduction of enteric methane emission. Further studies are warranted to explore the impact of diet on the distribution of rumen methanogens between the host species within and across different environmental conditions.

Assessment of intracellular reactive oxygen species (ROS) is important for evaluating the developmental ability of cumulus-oocyte complexes (COC) and embryos. Although, fluorescence-based 2',7'-dichlorodihydrofluorescein diacetate (DCFH-DA) staining method is used widely for detecting intracellular ROS in COC and embryos, it is associated with several limitations. This study aimed to develop an alternative method for detecting and quantifying intracellular ROS in oocytes, cumulus cells and embryos based on nitroblue tetrazolium (NBT) staining and bright-field microscopy. Nitroblue tetrazolium reacts with ROS and forms formazan precipitate that can be detected as dark purple/blue spots under bright-field microscope. Ovine COC were matured in vitro without (control) or with the supplementation of Interleukin-7 (IL-7; for stimulating intracellular ROS), Tempol (superoxide scavenger) or combination of IL-7 and Tempol. The matured COC were stained with NBT and the formation of intracellular formazan precipitates was assessed. Additionally, the matured COC were stained with DCFH-DA to compare the level of intracellular ROS. Further, ovine embryos (8-cell, morula, and degenerating) were generated in vitro and stained with NBT for assessing intracellular ROS. The level of intracellular ROS was expressed as the proportion (%) of the NBT stained area of oocytes, compact cumulus cell masses or embryos. The proportions of NBT stained area in the matured oocytes and cumulus cells was found significantly lesser in the control as compared to the IL-7 (1 and 5 ng/ml) treated groups. A similar trend in the intracellular ROS level was also observed in the matured COC, when assessed based on the DCFH-DA staining. Following the treatment with Tempol (100 mM), negligible NBT stained area in oocytes and cumulus cells was observed. The NBT staining patterns of the oocytes and cumulus cells following the combined treatment with IL-7 (5 ng/ml) and Tempol (10 and 25 mM) were comparable with that of the control. The proportion of NBT stained area did not differ significantly between the 8-cell embryos and morula, but was found significantly greater in the degenerating embryos. In conclusion, the developed NBT staining method was found effective for detecting and interpreting the level of intracellular ROS in oocytes, cumulus cells and embryos. This method can be used as an alternative to the DCFH-DA staining method.

This study aimed to assess the effect of the insulin-like grow factor 1 (IGF-1) treatment during

Aim: The aim of the study was to explore the anti-methanogenic potential of phyto-sources from Northeast region of the country and assess the effect on rumen fermentation characteristics and protozoa for their likely inclusion in animal diet to reduce methane emission. Materials and Methods: Twenty phyto-sources were collected from Northeast state, Assam, during March to April 2014. Phyto-sources were analyzed for their tannin content followed by screening for methane mitigation potential using in vitro system. The effect of tannin on methane production and other fermentation parameters was confirmed by attenuating the effect of tannin with polyethylene glycol (PEG)-6000 addition. About 200 mg dried phyto-source samples were incubated for 24 h in vitro, and volume of gas produced was recorded. The gas sample was analyzed on gas chromatograph for the proportion of methane in the sample. The effect of phyto-sources on rumen fermentation characteristics and protozoal population was determined using standard methodologies. Results: Results from studies demonstrated that Litchi chinensis, Melastoma malabathricum, Lagerstroemia speciosa, Terminalia chebula, and Syzygium cumini produced comparatively less methane, while Christella parasitica, Leucas linifolia, Citrus grandis, and Aquilaria malaccensis produced relatively more methane during in vitro incubation. An increase (p

With artificial insemination (AI) and other precision dependent assisted reproductive technologies (ART) being followed in large scale in human and animal reproduction, assessing semen quality and fertilizability is under continuous scrutiny. Various tests have been developed to predict semen quality, but so far no single, highly reliable test is available. In this regard, transcriptomic profiling of spermatozoa assumes significance as it carries the information about spermatogenesis, sperm function, and paternal roles in post-fertilization events. Human spermatozoal transcriptome profiling has been carried out on a large number of individuals to predict the semen quality. A study in human indicated that the outcome of some idiopathic couples seeking reproductive care could be helped using transcriptomic profiling of spermatozoa. Such studies have a direct impact on the bovine dairy industry, wherein AI is practiced. Limited studies in bovine spermatozoal transcriptome profiling have revealed that the spermatozoa contain various classes of RNA, like in human. Approximately 13,000 bovine genes yield a series of spermatozoal transcripts, of which most are fragmented in nature. Their abundance is indicative of the timing of events associated with spermatogenesis, e.g., PRM1, IGF1, BMP2; sperm function, TSSK6, CRISP, HSFY2; fertility, UBE2D3, Integrin-β, LDC-1; and embryonic development, miR34c-5p, BCL2L11, BRCA1. The most abundant translated bovine transcripts are BSP3 and SPATA18, and are involved in regulation of germ cell development and the maintenance of chromatin integrity during spermatogenesis respectively. The presence of transcripts associated with placental development, e.g., placental associated glycoproteins (PAGs) have suggested their possible influence beyond early embryonic development. Changes in transcript levels like RPL31 and PRKCE that increase, and PRM1 that decreases, during cryopreservation need to be defined in order to optimize cryopreservation and fertility yield. Spermatozoal transcriptome profiling with validation studies are warranted in large numbers of animals to elucidate their significance for selecting fertile bulls for the breeding program. Abbreviations: AI: artificial insemination; BSE: breeding soundness evaluation; cfs-mRNA: cell-free seminal mRNA; piRNA: PIWI-interacting RNA; tRNA: transfer RNA; fg: femtogram; TPM: transcripts per million reads; RPKM: reads per kilobase million; rRNA: ribosomal RNA; mt-RNA: mitochondrial RNA; lncRNA: long non-coding RNA; sncRNA: small noncoding RNA; snoRNA: small nucleolar RNA; snRNA: small nuclear RNA; miRNA: microRNA; snaR: small NF90-associated RNAs; SINES: short interspersed nuclear elements; LINES: long interspersed nuclear elements; MER: medium reiterated sequence; F1 offspring: filial 1 offspring; PAGs: placental associated glycoproteins; TCP: Transcription factor T complex protein; BSP3: bovine seminal plasma protein 3; SCNT: somatic cell nuclear transfer; qPCR: quantitative (real-time) polymerase chain reaction; SSH: suppression subtractive hybridization; SNP: single nucleotide polymorphism; 2-DE: 2 dimensional gel electrophoresis; LC-MS/MS: liquid chromatography-tandem mass spectrometry.

Utilization of energy-rich crop residues by ruminants is restricted by the presence of lignin, which is recalcitrant to digestion. Application of lignin degrading enzymes on the lignocellulosic biomass exposes the cellulose for easy digestion by ruminants. Laccases have been found to be considerably effective in improving the digestibility by way of delignification. However, laccase yields from natural hosts are not sufficient for industrial scale applications, which restricts their use. A viable option would be to express the laccase gene in compatible hosts to achieve higher production yields. A codon-optimized synthetic variant of Schizophyllum commune laccase gene was cloned into a pPIC9K vector and expressed in P. pastoris GS115 (his4) under the control of an alcohol oxidase promoter. Colonies were screened for G418 resistance and the methanol utilization phenotype was established. The transformant yielded a laccase activity of 344 U·mL-1 after 5 days of growth at 30°C (0.019 g·mL-1 wet cell weight). The laccase protein produced by the recombinant Pichia clone was detected as two bands with apparent molecular weights of 55 kDa and 70 kDa on SDS-PAGE. Activity staining on native PAGE confirmed the presence of bioactive laccase. Treatment of five common crop residues with recombinant laccase recorded a lignin loss ranging between 1.64% in sorghum stover, to 4.83% in finger millet, with an enhancement in digestibility ranging between 8.71% in maize straw to 24.61% in finger millet straw. Treatment with recombinant laccase was effective in enhancing the digestibility of lignocellulosic biomass for ruminant feeding through delignification. To date, a number of hosts have been adventured to produce laccase in large quantities, but, to our knowledge, there are no reports of the expression of laccase protein from Schizophyllum commune in Pichia pastoris, and also on the treatment of crop residues using recombinant laccase for ruminant feeding.

An in vivo study was conducted to compare the enteric methane emissions and diversity of ruminal methanogens in cattle and buffaloes kept in the same environment and fed on the same diet. Six cattle and six buffaloes were fed on a similar diet comprising Napier (Pennisetum purpureum) green grass and concentrate in 70:30. After 90 days of feeding, the daily enteric methane emissions were quantified by using the SF6 technique and ruminal fluid samples from animals were collected for the diversity analysis. The daily enteric methane emissions were significantly greater in cattle as compared to buffaloes; however, methane yields were not different between the two species. Methanogens were ranked at different taxonomic levels against the Rumen and Intestinal Methanogen-Database. The archaeal communities in both host species were dominated by the phylum Euryarchaeota; however, Crenarchaeota represented Methanobacteriales were most prominent and their proportion did not differ between the two hosts. Methanomicrobiales and Methanomassillicoccales constituted the second largest group of methanogens in cattle and buffaloes, respectively. Methanocellales (Methanocella arvoryza) were exclusively detected in the buffaloes. At the species level, Methanobrevibacter gottschalkii had the highest abundance (55–57%) in both the host species. The relative abundance of Methanobrevibacter wolinii between the two hosts differed significantly. Methanosarcinales, the acetoclastic methanogens were significantly greater in cattle than the buffaloes. It is concluded that the ruminal methane yield in cattle and buffaloes fed on the same diet did not differ. With the diet used in this study, there was a limited influence (

Tamarind seed husk, an agricultural waste, was evaluated both in vitro & in vivo as a methane-ameliorating agent. Basal diets for in vitro study were formulated using finger millet straw and concen...

The present study was undertaken to explore the methane reduction potential of phyto-sources from the foothills of Himalayan region. The qualitative screening of phyto-sources confirmed the presence of tannins in ~ 80% of the samples. Similarly, most of the phyto-samples were also possesses flavanoids (66%) and terpenoids (94%); however, none of the samples consist saponins or phlobatannins. The highest tannins concentration was reported in Terminalia chebula (245 g/kg DM), Zanthoxylum alatum (219 g/kg DM) and Punica granatum (207 g/kg DM). Phyto-sources such as Pittosporum eriocarpum, Prunusdomestica and Berberis lycium contain condensed and hydrolysable tannins in nearly equal proportions and comparatively produce lesser methane than non-tanniniferous phyto-sources sources or phyto-sources which possess either condensed or hydrolysable tannins. The study established that entodinomorphs were most vulnerable protozoa to tanniniferous phyto-sources. The attenuation of tannins impact through polyethylene glycol (PEG-6000) addition revealed a substantial increase in total volatile fatty acids (up to 23%) and ammonia nitrogen (up to 50%). It can be inferred from the study that Prunus domestica, Berberis lycium and Terminalia chebula due to their methane mitigation potential can be incorporated in animal feed for reducing methane emission. The present study unequivocally demonstrated that tannins-containing phyto-sources could be of great interest in the development of novel anti-methanogenic feed additives. However, the optimization of level of inclusion for the selected phyto-sources in animals diet should be studied.

The present work focuses on the value addition of cotton stalks through xylan extraction and enzymatic production of xylooligosaccharides (XOS); a pentose based prebiotic. Chemical analysis reveale...

Utilization of energy-rich crop residues by ruminants is restricted by the presence of lignin, which is recalcitrant to digestion. Application of lignin degrading enzymes on the lignocellulosic biomass exposes the cellulose for easy digestion by ruminants. Laccases have been found to be considerably effective in improving the digestibility by way of delignification. However, laccase yields from natural hosts are not sufficient for industrial scale applications, which restricts their use. A viable option would be to express the laccase gene in compatible hosts to achieve higher production yields. A codon-optimized synthetic variant of Schizophyllum commune laccase gene was cloned into a pPIC9K vector and expressed in P. pastoris GS115 (his4) under the control of an alcohol oxidase promoter. Colonies were screened for G418 resistance and the methanol utilization phenotype was established. The transformant yielded a laccase activity of 344 U·mL

The highly pathogenic avian influenza (HPAI) H5N1 virus, currently circulating in Asia, causes severe disease in domestic poultry as well as wild birds like crow. However, the molecular pathogenesis of HPAIV infection in crows and other wild birds is not well known. Thus, as a step to explore it, a comprehensive global gene expression analysis was performed on crow lungs, infected with HPAI H5N1 crow isolate (A/Crow/India/11TI11/2011) using high throughput next generation sequencing (NGS) (GS FLX Titanium XLR70). The reference genome of crow is not available, so RNA seq analysis was performed on the basis of a de novo assembled transcriptome. The RNA seq result shows, 4052 genes were expressed uniquely in noninfected, 6277 genes were expressed uniquely in HPAIV infected sample and of the 6814 genes expressed in both samples, 2279 genes were significantly differentially expressed. Our transcriptome profile data allows for the ability to understand the molecular mechanism behind the recent lethal HPAIV outbreak in crows which was, until recently, thought to cause lethal infections only in gallinaceous birds such as chickens, but not in wild birds. The pattern of differentially expressed genes suggest that this isolate of H5N1 virus evades the host innate immune response by attenuating interferon (IFN)-inducible signalling possibly by down regulating the signalling from type I IFN (IFNAR1 and IFNAR2) and type II IFN receptors, upregulation of the signalling inhibitors suppressor of cytokine signalling 1 (SOCS1) and SOCS3 and altering the expression of toll-like receptors (TLRs). This may be the reason for disease and mortality in crows.

The growing demands of novel food products for well-being and age related issues coupled with increasing health care expenditure has attracted global attention on prebiotics. During the end of twentieth century, a great concern was expressed for transfer of antibiotic resistance genes from animal to human through food chains leading to the concept of “preventive medication”. Xylooligosaccharides (XOS) is the only nutraceutical that can be produced from lignocellulosic biomass. Production of XOS from agricultural residues offers great scope to the nutraceutical industries as the raw material is cheap and abundantly available. The major advantages of XOS consumption, apart from selective growth stimulation of beneficial gut microflora, include reduction of blood glucose and cholesterol, reduced pro-carcinogenic enzymes in gastrointestinal tract, enhanced mineral absorption from large intestine and immune-stimulation. The sweet taste of XOS enables it to be used as an artificial sweetener. Owing to the ban on antibiotics as a feed supplement in livestock, the XOS could be future alternatives to guard gastrointestinal tract from the onslaught of pathogenic microflora. This will sustain the productivity and improve the quality of animal products to fulfil the demands of value added livestock products. Therefore, XOS could be the future sought after molecules in preventive medicine.

Cumulus cells (CC) play important roles in oocyte development and cumulus expressed genes can be used as markers for oocyte quality. This study aimed to investigate temporal changes in the expression of cumulus marker genes during oocyte maturation as possible biomarkers of embryo developmental competence in ovine. Gene expression was assessed in the CC of the BCB+ (developmentally competent) and BCB- (developmentally poor) oocytes at 0, 12, and 24 h of in vitro maturation (IVM). Further, the association between the temporal cumulus gene expression and in vitro oocyte and embryo development was assessed. The maturation and blastocyst formation rates were found significantly greater for the BCB+ than the BCB- oocytes. At the 0 h of IVM, a significant upregulation in the expression of PTGS2, STAR, SDC2, LHR, FGF2, BCL2, IL7RA, HSPA1A, and IFNT was observed in the CC of the poor (BCB-) as compared to the competent (BCB+) oocytes. In contrast, it was observed that as maturation progressed, the cumulus expression of most of the favorable genes was reduced and was found significantly downregulated at the completion of IVM in the poor as compared to the competent oocytes. The study revealed noticeable differences in the cumulus gene expression profile at different stages of IVM between ovine oocytes of differential developmental ability. The results indicated that the loss of cumulus gene expression along the maturation period in the poor oocytes was related to their intrinsic poor quality in the ovarian follicle.

Mammalian spermatozoa deliver various classes of RNAs to the oocyte during fertilization, and many of them may regulate fertility. The objective of the present study was to determine the composition and abundance of spermatozoal transcripts in fresh bull semen. The entire transcriptome of the spermatozoa from bulls (n = 3) was sequenced using two different platforms (Ion Proton and Illumina) to identify the maximum number of genes present in the spermatozoa. The bovine spermatozoa contained transcripts for 13,833 genes (transcripts per million, TPM > 10). Both intact and fragmented transcripts were found. These spermatozoal transcripts were associated with various stages of spermatogenesis, spermatozoal function, fertilization, and embryo development. The presence of intact transcripts of pregnancy-associated glycoproteins (PAGs) in the spermatozoa suggest a possible influence of sperm transcripts beyond early embryonic development. The specific regions (exon, intron, and exon-intron) of the particular spermatozoal transcripts might help regulate fertilization. This study demonstrates that the use of two different RNA-seq platforms provides a comprehensive profile of bovine spermatozoal RNA. Spermatozoal RNA profiling may be useful as a non-invasive method to delineate possible causes of male infertility and to predict fertility in a manner that is more effective than the conventional methods.

Prebiotics are fast emerging as health-promoting supplements.The study aimed tosculpture xylan from the corn cobs followed by xylooligosaccharides (XOS) pro-duction by enzymatic process. Application of 16% NaOH with steam enabledalmost 90% recovery of original xylan contents. Commercial xylanase was used tohydrolyze xylan into XOS such as xylobiose (X 2 ) and xylotriose (X 3 ). Responsesurface modeling (RSM) was adopted to minimize xylose and maximize X 2 andX 3 .According to RSM analysis,maximum X 2 yield (1.208 mg/mL) was obtained atpH 5.97, temperature 41.22C, enzyme dose 7.28 U for 17.31 h of hydrolysis.However, highest (0.715 mg/mL) X 3 production was recorded at pH 5.91, tem-perature 40.87C, enzyme dose of 5.83 U for 16.59 h of incubation. Application ofNaOH (16%) coupled with steam enabled corn cobs to release 90% of originalxylan that could be enzymatically converted into prebiotics such as XOS. PRACTICAL APPLICATIONS Apprehension against modern therapeutic agents coupled with increased health-care cost has encouraged the people to look for plant sourced bioactivecompounds such as prebiotic to maintain gut health and well-being.Xylooligosaccharides (XOS) occupy significant niche because its production prin-cipally depend on renewable agricultural wastes or by-products.As xylan has mul-tiple applications, the present process of xylan extraction could have greatersignificance as it is able to extract approximately 90% of original xylan. Applica-tion of commercial xylanase over corn cobs xylan leads to the production of XOScomprising of xylobiose and xylotriose. Adoption of enzymatic process for XOSproduction from the corn cobs xylan has diverse magnitude: one way it willdispose the wastes and other way benefit human population through prebioticeffects.

The effect of alkali viz., sodium hydroxide and potassium hydroxide, on the recovery of xylan from sugarcane bagasse under two different conditions namely overnight incubation at room temperature and autoclaving was investigated. Conditions for the enzymatic cleavage of the extracted xylan leading to the best yields of xylooligosaccharides was investigated using a fixed substrate concentration (2%, w/v) and varied inputs of other critical factors like pH, temperature, enzyme dose and reaction time. The sugarcane bagasse constituted of 98.99 ± 0.01% organic matter, 35.67 ± 0.15% cellulose, 23.22 ± 0.05% hemicellulose, 6.04 ± 0.06% lignin and 2.3 ± 0.01% protein. The highest xylan recovery of 85% was attained using 12% sodium hydroxide combined with steam application. Analyses of the enzymatic hydrolyzate showed the presence of XOS of varying degree of polymerization falling in the range of 2–3. The maximum conversion to XOS was observed at temperature of 40 °C, pH of 4 with an enzyme dose of 2.65 U and a reaction time of 8 h. The response surface analysis predicted ideal condition viz., temperature 40.99 °C, pH 4.92, enzyme dose 3.13 U and reaction time 19.19 h for maximizing xylobiose yield, while for maximum xylotriose yields the ideal variables were 40.37 °C, pH 4.13, enzyme dose 5.89 U and an incubation time of 18.14 h. The findings established the suitability of sugarcane bagasse as a raw material for extraction of xylan vis a vis its conversion into XOS.

Pigeon pea (Cajanus cajan) is a perennial plant widely cultivated in tropical and subtropical regions of many countries. The present studies aimed to produce xylooligosaccharides (XOS) from pigeon pea stalks in order to do value addition. The chemical analysis of stalks revealed 18.33 ± 1.40 % hemicelluloses in addition to cellulose, protein, and lignin. Sodium hydroxide coupled with steam application enabled almost 96 % recovery of original xylan, present in the pigeon pea stalks. Enzymatic hydrolysis of xylan led to production of XOS namely, xylobiose and xylotriose. Response surface model indicated a maximum yield of xylobiose (0.502 mg/ml) under the hydrolysis conditions of pH 4.91, temperature at 48.11 °C, enzyme dose at 11.01 U, and incubation time at 15.65 h. The ideal conditions for higher xylotriose yield (0.204 mg/ml) were pH 5.44, temperature at 39.29 °C, enzyme dose at 3.23 U, and incubation time at 15.26 h. The present investigation was successful in assessing the prospect of using pigeon pea stalks as a raw material for xylan extraction vis-à-vis XOS production.

Corn cobs are major byproduct of maize processing industries. For value addition of maize byproducts, the present paper aims at extracting xylan from corn cobs and subsequent production of xylooligosaccharides (XOS). Compositional determination of corn cobs revealed 38.78% hemicellulose, 27.71% cellulose and 9.4% lignin. Recovery of xylan increased with increasing concentration of alkali during extraction. The extracted xylan was subjected to acidic hydrolysis to yield XOS. HPLC analysis of hydrolysate revealed increased production of XOS with time, but prolonged incubation resulted in higher amount of xylose. Four probiotic strains were used for undertaking in vitro evaluation of the prebiotic efficacy of XOS. XOS ensured higher growth rate for Enterococcus faecium as compared to other probionts, while fructooligosaccharides (FOS) supported higher proliferation of Lactobacillus viridiscens . This method of xylan extraction and production of XOS offers scope for value addition to the corn byproducts.

In this study, a process for producing XOS from Sehima nervosum grass was developed. The grass contains 28.1% hemicellulose. NaOH and steam application yielded 98% of original xylan in contrast to 85% by KOH application. Hydrolysis of xylan with commercial xylanase caused breakdown into XOS comprising of xylobiose, xylotriose along with xylose. Response surface model (RSM) revealed highest xylobiose yield (11 g/100 g xylan) at pH 5.03, temperature 45.19 °C, reaction time 10.11 h with enzyme dose 17.41 U. Similarly for maximizing xylotriose yield, ideal hydrolysis conditions were pH 5.11, temperature 40.33 °C, reaction time 16.55 h with enzyme dose 13.20 U. A two step process encompassing xylan fractionation and enzymatic hydrolysis enabled XOS production from the S. nervosum grass.

Endo-β-1, 4-xylanases is thought to be of great significance for several industries namely paper, pharmaceuticals, food, feed etc. in addition to better utilization of lignocellulosic biomass. The present investigation was aimed to develop an easy, simple and efficient assay technique for endo-β-1, 4-xylanases secreted by the aerobic fungi. Under the proposed protocol, 9 g/L xylan containing agar was prepared in 100 mM phosphate buffer at different pH (4.5, 5.5 and 6.5). The sterilized xylan agar was dispensed in 90 mm petri dishes. 100 µl of culture supernatant of 12 fungal isolates was added to the wells and left overnight at 31±1(0)C. The petri dishes were observed for zone of clearance by naked eye and diameter was measured. Congo red solution (1 g/L) was applied over the petri dishes as per the established protocol and thereafter plates were flooded with 1M Sodium chloride solution for the appearance of zone of clearance. The diameter for zone of clearance by the proposed method and the established protocol was almost identical and ranged from 21 to 42 mm at different pH depending upon the activity of endo-β-1, 4-xylanases. Change of pH towards alkaline side enabled similar or marginal decrease of diameter for the zone of clearance in most of the fungal isolates. The specific activities of these fungal isolates varied from 1.85 to 11.47 IU/mg protein. The present investigation revealed that the proposed simple diffusion technique gave similar results as compared to the established Congo red assay for endo-β-1, 4-xylanases. Moreover, the present technique avoided the cumbersome steps of staining by Congo red and de-staining by sodium chloride.

Endo-β-1, 4-xylanases is thought to be of great significance for several industries namely paper, pharmaceuticals, food, feed etc. in addition to better utilization of lignocellulosic biomass. The present investigation was aimed to develop an easy, simple and efficient assay technique for endo-β-1, 4-xylanases secreted by the aerobic fungi. Under the proposed protocol, 9 g/L xylan containing agar was prepared in 100 mM phosphate buffer at different pH (4.5, 5.5 and 6.5). The sterilized xylan agar was dispensed in 90 mm petri dishes. 100 µl of culture supernatant of 12 fungal isolates was added to the wells and left overnight at 31±1(0)C. The petri dishes were observed for zone of clearance by naked eye and diameter was measured. Congo red solution (1 g/L) was applied over the petri dishes as per the established protocol and thereafter plates were flooded with 1M Sodium chloride solution for the appearance of zone of clearance. The diameter for zone of clearance by the proposed method and the established protocol was almost identical and ranged from 21 to 42 mm at different pH depending upon the activity of endo-β-1, 4-xylanases. Change of pH towards alkaline side enabled similar or marginal decrease of diameter for the zone of clearance in most of the fungal isolates. The specific activities of these fungal isolates varied from 1.85 to 11.47 IU/mg protein. The present investigation revealed that the proposed simple diffusion technique gave similar results as compared to the established Congo red assay for endo-β-1, 4-xylanases. Moreover, the present technique avoided the cumbersome steps of staining by Congo red and de-staining by sodium chloride.

The enzyme endo-inulinase hydrolyzes inulin to short chain fructooligosaccharides (FOS) that are potential prebiotics with many health promoting benefits. Although the raw materials for inulin production are inexpensive and readily available, commercial production of FOS from inulin is limited due to inadequate availability of the enzyme source. This study aimed to identify the fungi capable of producing endo-inulinase based on the in silico analysis of proteins retrieved from non-redundant protein sequence database. The endo-inulinase of Aspergillus ficuum was used as reference sequence. The amino acid sequences with >90% sequence coverage, belonging to different fungi were retrieved from the database and used for constructing three-dimensional (3D) protein models using SWISS-MODEL and Bagheerath H. The 3D models of comparable quality as that of the reference endo-inulinase were selected based on QMEAN Z score. The selected models were evaluated and validated for different structural and functional qualities using Pro-Q, ProSA, PSN-QA, VERIFY-3D, PROCHECK, PROTSAV metaserver, STRAP, molecular docking, and molecular dynamic simulation analyses. A total of 230 proteins belonging to 53 fungal species exhibited sequence coverage >90%. Sixty one protein sequences with >60% sequence identity were modeled as endo-inulinase with higher QMEAN Z Score. The evaluations and validations of these 61 selected models for different structural and functional qualities revealed that 60 models belonging to 22 fungal species exhibited native like structure and unique motifs and residues as that of the reference endo-inulinase. Further, these models also exhibited similar kind of interaction between the active site around the conserved glutamate residue and substrate as that of the reference endo-inulinase. In conclusion, based on the current study, 22 fungal species could be identified as endo-inulinase producer. Nevertheless, further biological assessment of their capability for producing endo-inulinase is imminent if they are to be used for commercial endo-inulinase production for application in FOS industry.